The Polyploid Gene Assembler (PGA), developed and tested in this study, represents a new strategy to perform gene-space assembly from complex genomes using low coverage DNA sequencing. The pipeline integrates reference-assisted loci and de novo assembly strategies to construct high-quality sequences focused on gene content. Pipeline validation was conducted with wheat (Triticum aestivum), a hexaploid species, using barley (Hordeum vulgare) as reference, that resulted in the identification of more than 90% of genes and several new genes. Moreover, PGA was used to assemble gene content in Saccharum spontaneum species, a parental lineage for hybrid sugarcane cultivars. Saccharum spontaneum gene sequence obtained was used to reference-guided transcriptome analysis of six different tissues. A total of 39,234 genes were identified, 60.4% clustered into known grass gene families. Thirty-seven gene families were expanded when compared with other grasses, three of them highlighted by the number of gene copies potentially involved in initial development and stress response. In addition, 3,108 promoters (many showing tissue specificity) were identified in this work. In summary, PGA can reconstruct high-quality gene sequences from polyploid genomes, as shown for wheat and S. spontaneum species, and it is more efficient than conventional genome assemblers using low coverage DNA sequencing.

中文翻译：

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使用多倍体基因装配体解开自发性酿酒酵母的复杂基因组。

在这项研究中开发和测试的多倍体基因装配体（PGA）代表了一种新策略，可以使用低覆盖率DNA测序从复杂基因组进行基因空间装配。该管道整合了参考辅助基因座和从头组装策略，以构建专注于基因内容的高质量序列。以大麦（Hordeum vulgare）为参考，对六倍体小麦（Triticum aestivum）进行了管道验证，结果鉴定出了90％以上的基因和几个新基因。此外，PGA被用于组装自发性蔗糖品种的基因内容，该品种是杂交甘蔗品种的亲本谱系。所获得的自发性酵母糖基因序列用于参考引导的六种不同组织的转录组分析。总共鉴定了39,234个基因，其中60个。4％聚集成已知的草基因家族。与其他草相比，该基因家族增加了37个，其中三个突出了可能参与初始发育和胁迫反应的基因拷贝数。另外，在这项工作中鉴定出3,108个启动子（许多显示组织特异性）。总而言之，PGA可以从多倍体基因组中重建高质量的基因序列，如小麦和自发链球菌物种所示，它比使用低覆盖率DNA测序的常规基因组组装器更有效。在这项工作中确定了108个启动子（许多显示组织特异性）。总而言之，PGA可以从多倍体基因组中重建高质量的基因序列，如小麦和自发链球菌物种所示，它比使用低覆盖率DNA测序的常规基因组组装器更有效。在这项工作中确定了108个启动子（许多显示组织特异性）。总而言之，PGA可以从多倍体基因组中重建高质量的基因序列，如小麦和自发链球菌物种所示，它比使用低覆盖率DNA测序的常规基因组组装器更有效。